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- PDB-5zca: Crystal structure of lambda repressor (1-20) fused with maltose-b... -

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Basic information

Entry
Database: PDB / ID: 5zca
TitleCrystal structure of lambda repressor (1-20) fused with maltose-binding protein
ComponentsRepressor protein cI,Maltose-binding periplasmic protein
KeywordsDNA BINDING PROTEIN / LAMBDA REPRESSOR / MALTOSE-BINDING PROTEIN / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / core promoter sequence-specific DNA binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / identical protein binding / membrane
Similarity search - Function
LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / CITRIC ACID / Repressor protein cI / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: Febs Open Bio / Year: 2018
Title: Co-translational folding of alpha-helical proteins: structural studies of intermediate-length variants of the lambda repressor
Authors: Hanazono, Y. / Takeda, K. / Miki, K.
History
DepositionFeb 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor protein cI,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5623
Polymers43,0281
Non-polymers5342
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint3 kcal/mol
Surface area16880 Å2
Unit cell
Length a, b, c (Å)48.956, 58.343, 124.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Repressor protein cI,Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 43027.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Repressor protein (residues 1-20), linker, and Maltose-binding periplasmic protein (residues 24-389)
Source: (gene. exp.) Escherichia phage lambda (virus), (gene. exp.) Escherichia coli (E. coli)
Gene: cI, lambdap88, malE, b4034, JW3994 / Strain: K12 / Production host: Escherichia coli (E. coli) / References: UniProt: P03034, UniProt: P0AEX9
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M triammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33855 / % possible obs: 100 % / Redundancy: 6.4 % / Rsym value: 0.083 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.817 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 1.801→45.566 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.215 1637 4.84 %
Rwork0.1729 --
obs0.1749 33794 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→45.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 36 360 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063193
X-RAY DIFFRACTIONf_angle_d1.0164357
X-RAY DIFFRACTIONf_dihedral_angle_d13.731217
X-RAY DIFFRACTIONf_chiral_restr0.049474
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8012-1.85420.29961070.24882647X-RAY DIFFRACTION99
1.8542-1.91410.28221390.2332628X-RAY DIFFRACTION100
1.9141-1.98250.2571250.20452629X-RAY DIFFRACTION100
1.9825-2.06180.26671210.1982679X-RAY DIFFRACTION100
2.0618-2.15570.26341340.18762639X-RAY DIFFRACTION100
2.1557-2.26930.21231420.19032648X-RAY DIFFRACTION100
2.2693-2.41150.22581450.18172644X-RAY DIFFRACTION100
2.4115-2.59770.24161540.17922667X-RAY DIFFRACTION100
2.5977-2.85910.19811350.16842683X-RAY DIFFRACTION100
2.8591-3.27270.21881550.16272691X-RAY DIFFRACTION100
3.2727-4.12280.16351370.14482731X-RAY DIFFRACTION100
4.1228-45.58010.20681430.16562871X-RAY DIFFRACTION100

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